Table 9. Immune module: significantly enriched gene sets.
| Gene set | OR (95% C.I.) | q-val |
| REACTOME_ADAPTIVE_IMMUNE_SYSTEM | 37 (9.3–170) | 0.001 |
| REACTOME_ANTIGEN_PROCESSING_CROSS_PRESENTATION | 97 (20–390) | 0.0019 |
| REACTOME_ANTIGEN_PRESENTATION_FOLDING_ASSEMBLY_AND_PEPTIDE_LOADING_OF_CLASS_I_MHC | 210 (33–980) | 0.0036 |
| REACTOME_THE_ROLE_OF_NEF_IN_HIV1_REPLICATION_AND_DISEASE_PATHOGENESIS | 140 (23–670) | 0.006 |
| REACTOME_IMMUNE_SYSTEM | 22 (5.5–100) | 0.006 |
| KEGG_CELL_ADHESION_MOLECULES_CAMS | 52 (11–210) | 0.0069 |
| GNF2_HLA-C | 110 (17–480) | 0.0094 |
| GNF2_INPP5D | 100 (17–460) | 0.0094 |
| GNF2_ITGAL | 100 (16–440) | 0.0094 |
| REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL | 89 (15–390) | 0.012 |
| RECEPTOR_COMPLEX | 76 (13–330) | 0.013 |
| GNF2_CD53 | 80 (13–350) | 0.013 |
| KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION | 76 (13–330) | 0.013 |
| PID_CD8TCRDOWNSTREAMPATHWAY | 80 (13–350) | 0.013 |
| PID_CD8TCRPATHWAY | 71 (12–310) | 0.014 |
| REACTOME_ER_PHAGOSOME_PATHWAY | 71 (12–310) | 0.014 |
| REACTOME_ENDOSOMAL_VACUOLAR_PATHWAY | 370 (32–2500) | 0.015 |
| DER_IFN_ALPHA_RESPONSE_UP | 66 (11–290) | 0.015 |
| PID_IL12_2PATHWAY | 65 (11–280) | 0.015 |
| BIOCARTA_TCRA_PATHWAY | 310 (27–2200) | 0.015 |
| REACTOME_NEF_MEDIATED_DOWNREGULATION_OF_MHC_CLASS_I_COMPLEX_CELL_SURFACE_EXPRESSION | 310 (27–2200) | 0.015 |
| REACTOME_TRANSLOCATION_OF_ZAP_70_TO_IMMUNOLOGICAL_SYNAPSE | 310 (27–2200) | 0.015 |
| DER_IFN_GAMMA_RESPONSE_UP | 61 (10–270) | 0.015 |
| BIOCARTA_CTL_PATHWAY | 270 (24–1600) | 0.018 |
| MODULE_293 | 270 (24–1600) | 0.018 |
| REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION | 27 (5.8–110) | 0.018 |
| IMMUNOLOGICAL_SYNAPSE | 230 (21–1400) | 0.021 |
| MODULE_143 | 210 (19–1200) | 0.025 |
| GNF2_MATK | 140 (14–820) | 0.043 |
| KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY | 38 (6.4–160) | 0.043 |
| SENGUPTA_EBNA1_ANTICORRELATED | 38 (6.4–160) | 0.043 |
| GNF2_ZAP70 | 130 (13–740) | 0.045 |
| BIOCARTA_CSK_PATHWAY | 130 (13–740) | 0.045 |
Significantly enriched gene sets, for the immune module found as significant in the UCEC data set. Q-values indicate significance of enrichment in the corresponding gene set by the genes in this module, calculated according to a one-sided Fisher’s exact test. Further details about these gene sets can be found from the website of the Broad Institute Molecular Signatures Database (http://www.broadinstitute.org).